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Bacterial community diversity and variation in spray water sources and the tomato fruit surface.

Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS - BMC Microbiol. (2011)

Bottom Line: The two water sources tested had a significantly different bacterial composition.Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia.Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 21201, USA. atelias@umd.edu

ABSTRACT

Background: Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production.

Results: The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.

Conclusions: Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

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Related in: MedlinePlus

OTU-based bacterial diversity analysis of water and crop samples. (A) Rarefaction curves displaying the average number of OTUs discovered by random sampling within each sample. We observe a higher diversity in all surface water samples (ws) relative to fruit surface and groundwater samples. (B) This increased diversity is also apparent through the Chao1 and Shannon diversity estimators. To avoid bias due to different sampling depths, we first rarefied the data by randomly selecting 1100 sequences from each sample. Note that Chao1 estimates for total species-level diversity in surface water samples consistently exceed 1000 species, while all other environments fall below 500.
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Figure 3: OTU-based bacterial diversity analysis of water and crop samples. (A) Rarefaction curves displaying the average number of OTUs discovered by random sampling within each sample. We observe a higher diversity in all surface water samples (ws) relative to fruit surface and groundwater samples. (B) This increased diversity is also apparent through the Chao1 and Shannon diversity estimators. To avoid bias due to different sampling depths, we first rarefied the data by randomly selecting 1100 sequences from each sample. Note that Chao1 estimates for total species-level diversity in surface water samples consistently exceed 1000 species, while all other environments fall below 500.

Mentions: To compute estimates of species-level diversity and perform comparisons between environments, all sequences were clustered into operational taxonomic units (OTUs) using Mothur [30] and a similarity threshold of 95% (see Methods). The total number of unique OTUs within each environment was 494 (pg), 399 (ps), 228 (wg) and 1342 (ws). After computing rarefaction curves for each sample (Figure 3A), we immediately observed that the surface water samples were significantly more diverse than the others, and that groundwater and fruit surface samples are indistinguishable in terms of diversity. Additionally, the Shannon diversity index and Chao1 estimator were calculated for each sample, and again we see that the ws samples are the most diverse at the OTU level (Figure 3B).


Bacterial community diversity and variation in spray water sources and the tomato fruit surface.

Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS - BMC Microbiol. (2011)

OTU-based bacterial diversity analysis of water and crop samples. (A) Rarefaction curves displaying the average number of OTUs discovered by random sampling within each sample. We observe a higher diversity in all surface water samples (ws) relative to fruit surface and groundwater samples. (B) This increased diversity is also apparent through the Chao1 and Shannon diversity estimators. To avoid bias due to different sampling depths, we first rarefied the data by randomly selecting 1100 sequences from each sample. Note that Chao1 estimates for total species-level diversity in surface water samples consistently exceed 1000 species, while all other environments fall below 500.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108269&req=5

Figure 3: OTU-based bacterial diversity analysis of water and crop samples. (A) Rarefaction curves displaying the average number of OTUs discovered by random sampling within each sample. We observe a higher diversity in all surface water samples (ws) relative to fruit surface and groundwater samples. (B) This increased diversity is also apparent through the Chao1 and Shannon diversity estimators. To avoid bias due to different sampling depths, we first rarefied the data by randomly selecting 1100 sequences from each sample. Note that Chao1 estimates for total species-level diversity in surface water samples consistently exceed 1000 species, while all other environments fall below 500.
Mentions: To compute estimates of species-level diversity and perform comparisons between environments, all sequences were clustered into operational taxonomic units (OTUs) using Mothur [30] and a similarity threshold of 95% (see Methods). The total number of unique OTUs within each environment was 494 (pg), 399 (ps), 228 (wg) and 1342 (ws). After computing rarefaction curves for each sample (Figure 3A), we immediately observed that the surface water samples were significantly more diverse than the others, and that groundwater and fruit surface samples are indistinguishable in terms of diversity. Additionally, the Shannon diversity index and Chao1 estimator were calculated for each sample, and again we see that the ws samples are the most diverse at the OTU level (Figure 3B).

Bottom Line: The two water sources tested had a significantly different bacterial composition.Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia.Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 21201, USA. atelias@umd.edu

ABSTRACT

Background: Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production.

Results: The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.

Conclusions: Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

Show MeSH
Related in: MedlinePlus